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Granath-Panelo M, Kajimura S. Mitochondrial heterogeneity and adaptations to cellular needs. Nat Cell Biol 2024; 26:674-686. [PMID: 38755301 DOI: 10.1038/s41556-024-01410-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 03/21/2024] [Indexed: 05/18/2024]
Abstract
Although it is well described that mitochondria are at the epicentre of the energy demands of a cell, it is becoming important to consider how each cell tailors its mitochondrial composition and functions to suit its particular needs beyond ATP production. Here we provide insight into mitochondrial heterogeneity throughout development as well as in tissues with specific energy demands and discuss how mitochondrial malleability contributes to cell fate determination and tissue remodelling.
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Affiliation(s)
- Melia Granath-Panelo
- Division of Endocrinology, Beth Israel Deaconess Medical Center, Harvard Medical School and Howard Hughes Medical Institute, Boston, MA, USA.
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Shingo Kajimura
- Division of Endocrinology, Beth Israel Deaconess Medical Center, Harvard Medical School and Howard Hughes Medical Institute, Boston, MA, USA.
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2
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Hu B, Jin H, Shi Y, Yu H, Wu X, Wang S, Zhang K. Single-cell RNA-Seq reveals the earliest lineage specification and X chromosome dosage compensation in bovine preimplantation embryos. FASEB J 2024; 38:e23492. [PMID: 38363564 DOI: 10.1096/fj.202302035rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 01/29/2024] [Accepted: 02/01/2024] [Indexed: 02/17/2024]
Abstract
Lineage specification and X chromosome dosage compensation are two crucial biological processes that occur during preimplantation embryonic development. Although extensively studied in mice, the timing and regulation of these processes remain elusive in other species, including humans. Previous studies have suggested conserved principles of human and bovine early development. This study aims to provide fundamental insights into these programs and the regulation using a bovine embryo model by employing single-cell transcriptomics and genome editing approaches. The study analyzes the transcriptomes of 286 individual cells and reveals that bovine trophectoderm/inner cell mass transcriptomes diverge at the early blastocyst stage, after cavitation but before blastocyst expansion. The study also identifies transcriptomic markers and provides the timing of lineage specification events in the bovine embryo. Importantly, we find that SOX2 is required for the first cell decision program in bovine embryos. Moreover, the study shows the occurrence of X chromosome dosage compensation from morula to late blastocyst and reveals that this compensation results from downregulation of X-linked genes in female embryonic cells. The transcriptional atlas generated by this study is expected to be widely useful in improving our understanding of mammalian early embryo development.
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Affiliation(s)
- Bingjie Hu
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hao Jin
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yan Shi
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Haotian Yu
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaotong Wu
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Shaohua Wang
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Kun Zhang
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
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3
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Karger A, Mansouri S, Leisegang MS, Weigert A, Günther S, Kuenne C, Wittig I, Zukunft S, Klatt S, Aliraj B, Klotz LV, Winter H, Mahavadi P, Fleming I, Ruppert C, Witte B, Alkoudmani I, Gattenlöhner S, Grimminger F, Seeger W, Pullamsetti SS, Savai R. ADPGK-AS1 long noncoding RNA switches macrophage metabolic and phenotypic state to promote lung cancer growth. EMBO J 2023; 42:e111620. [PMID: 37545364 PMCID: PMC10505917 DOI: 10.15252/embj.2022111620] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/06/2023] [Accepted: 07/08/2023] [Indexed: 08/08/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) influence the transcription of gene networks in many cell types, but their role in tumor-associated macrophages (TAMs) is still largely unknown. We found that the lncRNA ADPGK-AS1 was substantially upregulated in artificially induced M2-like human macrophages, macrophages exposed to lung cancer cells in vitro, and TAMs from human lung cancer tissue. ADPGK-AS1 is partly located within mitochondria and binds to the mitochondrial ribosomal protein MRPL35. Overexpression of ADPGK-AS1 in macrophages upregulates the tricarboxylic acid cycle and promotes mitochondrial fission, suggesting a phenotypic switch toward an M2-like, tumor-promoting cytokine release profile. Macrophage-specific knockdown of ADPGK-AS1 induces a metabolic and phenotypic switch (as judged by cytokine profile and production of reactive oxygen species) to a pro-inflammatory tumor-suppressive M1-like state, inhibiting lung tumor growth in vitro in tumor cell-macrophage cocultures, ex vivo in human tumor precision-cut lung slices, and in vivo in mice. Silencing ADPGK-AS1 in TAMs may thus offer a novel therapeutic strategy for lung cancer.
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Affiliation(s)
- Annika Karger
- Max Planck Institute for Heart and Lung ResearchMember of the German Center for Lung Research (DZL), Member of the Cardio‐Pulmonary Institute (CPI)Bad NauheimGermany
- Institute for Lung Health (ILH)Justus Liebig UniversityGiessenGermany
| | - Siavash Mansouri
- Max Planck Institute for Heart and Lung ResearchMember of the German Center for Lung Research (DZL), Member of the Cardio‐Pulmonary Institute (CPI)Bad NauheimGermany
- Institute for Lung Health (ILH)Justus Liebig UniversityGiessenGermany
| | - Matthias S Leisegang
- Institute for Cardiovascular Physiology, Medical FacultyGoethe University FrankfurtFrankfurtGermany
| | - Andreas Weigert
- Institute of Biochemistry I, Faculty of MedicineGoethe University FrankfurtFrankfurtGermany
- Frankfurt Cancer Institute (FCI)Goethe University FrankfurtFrankfurtGermany
| | - Stefan Günther
- Max Planck Institute for Heart and Lung ResearchMember of the German Center for Lung Research (DZL), Member of the Cardio‐Pulmonary Institute (CPI)Bad NauheimGermany
| | - Carsten Kuenne
- Max Planck Institute for Heart and Lung ResearchMember of the German Center for Lung Research (DZL), Member of the Cardio‐Pulmonary Institute (CPI)Bad NauheimGermany
| | - Ilka Wittig
- Functional Proteomics, Medical SchoolGoethe University FrankfurtFrankfurtGermany
| | - Sven Zukunft
- Institute for Vascular Signalling, Centre for Molecular MedicineGoethe UniversityFrankfurtGermany
| | - Stephan Klatt
- Institute for Vascular Signalling, Centre for Molecular MedicineGoethe UniversityFrankfurtGermany
| | - Blerina Aliraj
- Institute of Biochemistry I, Faculty of MedicineGoethe University FrankfurtFrankfurtGermany
| | - Laura V Klotz
- Translational Lung Research Center (TLRC), Member of the DZLHeidelbergGermany
- Department of Thoracic SurgeryThoraxklinik at the University Hospital HeidelbergHeidelbergGermany
| | - Hauke Winter
- Translational Lung Research Center (TLRC), Member of the DZLHeidelbergGermany
- Department of Thoracic SurgeryThoraxklinik at the University Hospital HeidelbergHeidelbergGermany
| | - Poornima Mahavadi
- Department of Internal MedicineMember of the DZL, Member of CPI, Justus Liebig UniversityGiessenGermany
| | - Ingrid Fleming
- Institute for Vascular Signalling, Centre for Molecular MedicineGoethe UniversityFrankfurtGermany
| | - Clemens Ruppert
- Department of Internal MedicineMember of the DZL, Member of CPI, Justus Liebig UniversityGiessenGermany
| | - Biruta Witte
- Department of General and Thoracic SurgeryUniversity Hospital GiessenGiessenGermany
| | - Ibrahim Alkoudmani
- Department of General and Thoracic SurgeryUniversity Hospital GiessenGiessenGermany
| | | | - Friedrich Grimminger
- Institute for Lung Health (ILH)Justus Liebig UniversityGiessenGermany
- Department of Internal MedicineMember of the DZL, Member of CPI, Justus Liebig UniversityGiessenGermany
| | - Werner Seeger
- Max Planck Institute for Heart and Lung ResearchMember of the German Center for Lung Research (DZL), Member of the Cardio‐Pulmonary Institute (CPI)Bad NauheimGermany
- Institute for Lung Health (ILH)Justus Liebig UniversityGiessenGermany
- Department of Internal MedicineMember of the DZL, Member of CPI, Justus Liebig UniversityGiessenGermany
| | - Soni Savai Pullamsetti
- Max Planck Institute for Heart and Lung ResearchMember of the German Center for Lung Research (DZL), Member of the Cardio‐Pulmonary Institute (CPI)Bad NauheimGermany
- Institute for Lung Health (ILH)Justus Liebig UniversityGiessenGermany
- Department of Internal MedicineMember of the DZL, Member of CPI, Justus Liebig UniversityGiessenGermany
| | - Rajkumar Savai
- Max Planck Institute for Heart and Lung ResearchMember of the German Center for Lung Research (DZL), Member of the Cardio‐Pulmonary Institute (CPI)Bad NauheimGermany
- Institute for Lung Health (ILH)Justus Liebig UniversityGiessenGermany
- Frankfurt Cancer Institute (FCI)Goethe University FrankfurtFrankfurtGermany
- Department of Internal MedicineMember of the DZL, Member of CPI, Justus Liebig UniversityGiessenGermany
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4
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Oddsson A, Sulem P, Sveinbjornsson G, Arnadottir GA, Steinthorsdottir V, Halldorsson GH, Atlason BA, Oskarsson GR, Helgason H, Nielsen HS, Westergaard D, Karjalainen JM, Katrinardottir H, Fridriksdottir R, Jensson BO, Tragante V, Ferkingstad E, Jonsson H, Gudjonsson SA, Beyter D, Moore KHS, Thordardottir HB, Kristmundsdottir S, Stefansson OA, Rantapää-Dahlqvist S, Sonderby IE, Didriksen M, Stridh P, Haavik J, Tryggvadottir L, Frei O, Walters GB, Kockum I, Hjalgrim H, Olafsdottir TA, Selbaek G, Nyegaard M, Erikstrup C, Brodersen T, Saevarsdottir S, Olsson T, Nielsen KR, Haraldsson A, Bruun MT, Hansen TF, Steingrimsdottir T, Jacobsen RL, Lie RT, Djurovic S, Alfredsson L, Lopez de Lapuente Portilla A, Brunak S, Melsted P, Halldorsson BV, Saemundsdottir J, Magnusson OT, Padyukov L, Banasik K, Rafnar T, Askling J, Klareskog L, Pedersen OB, Masson G, Havdahl A, Nilsson B, Andreassen OA, Daly M, Ostrowski SR, Jonsdottir I, Stefansson H, Holm H, Helgason A, Thorsteinsdottir U, Stefansson K, Gudbjartsson DF. Deficit of homozygosity among 1.52 million individuals and genetic causes of recessive lethality. Nat Commun 2023; 14:3453. [PMID: 37301908 PMCID: PMC10257723 DOI: 10.1038/s41467-023-38951-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
Genotypes causing pregnancy loss and perinatal mortality are depleted among living individuals and are therefore difficult to find. To explore genetic causes of recessive lethality, we searched for sequence variants with deficit of homozygosity among 1.52 million individuals from six European populations. In this study, we identified 25 genes harboring protein-altering sequence variants with a strong deficit of homozygosity (10% or less of predicted homozygotes). Sequence variants in 12 of the genes cause Mendelian disease under a recessive mode of inheritance, two under a dominant mode, but variants in the remaining 11 have not been reported to cause disease. Sequence variants with a strong deficit of homozygosity are over-represented among genes essential for growth of human cell lines and genes orthologous to mouse genes known to affect viability. The function of these genes gives insight into the genetics of intrauterine lethality. We also identified 1077 genes with homozygous predicted loss-of-function genotypes not previously described, bringing the total set of genes completely knocked out in humans to 4785.
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Affiliation(s)
| | | | | | - Gudny A Arnadottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | | | | | - Henriette Svarre Nielsen
- Deptartment of Obstetrics and Gynecology, Copenhagen University Hospital, Hvidovre, Denmark
- Department of Clinical Medicine, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
| | - David Westergaard
- Deptartment of Obstetrics and Gynecology, Copenhagen University Hospital, Hvidovre, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Methods and Analysis, Statistics Denmark, Copenhagen, Denmark
| | - Juha M Karjalainen
- Institute for Molecular Medicine, Finland, University of Helsinki, Helsinki, Finland
| | | | | | | | | | | | | | | | | | - Kristjan H S Moore
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | - Helga B Thordardottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | - Ida Elken Sonderby
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
- NORMENT Centre, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental disorders, University of Oslo, Oslo, Norway
| | - Maria Didriksen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Pernilla Stridh
- Neuroimmunology Unit, Department of Clinical Neuroscience, Center of Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Jan Haavik
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Bergen Center of Brain Plasticity, Division of Psychiatry, Haukeland University Hospital, Bergen, Norway
| | - Laufey Tryggvadottir
- Icelandic Cancer Registry, Icelandic Cancer Society, Reykjavik, Iceland
- Faculty of Medicine, BMC, Laeknagardur, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Oleksandr Frei
- NORMENT Centre, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | | | - Ingrid Kockum
- Neuroimmunology Unit, Department of Clinical Neuroscience, Center of Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Henrik Hjalgrim
- Department of Clinical Medicine, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | | | - Geir Selbaek
- Norwegian National Centre of Ageing and Health, Vestfold Hospital Trust, Tonsberg, Norway
- Department of Geriatric Medicine, Oslo University Hospital, Oslo, Norway
- Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Mette Nyegaard
- Deptartment of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Thorsten Brodersen
- Department of Clinical Immunology, Zealand University Hospital, Koge, Denmark
| | - Saedis Saevarsdottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Tomas Olsson
- Neuroimmunology Unit, Department of Clinical Neuroscience, Center of Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Kaspar Rene Nielsen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | - Asgeir Haraldsson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Children's Hospital Iceland, Landspitali University Hospital, Reykjavik, Iceland
| | - Mie Topholm Bruun
- Department of Clinical Immunology, Odense University Hospital, Odense, Denmark
| | - Thomas Folkmann Hansen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Neurology, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Thora Steingrimsdottir
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Rikke Louise Jacobsen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Rolv T Lie
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Srdjan Djurovic
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
- NORMENT Centre, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental disorders, University of Oslo, Oslo, Norway
| | - Lars Alfredsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Soren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Pall Melsted
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Bjarni V Halldorsson
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- School of Science and Engineering, Reykjavik University, Reykjavik, Iceland
| | | | | | - Leonid Padyukov
- Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
| | - Karina Banasik
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Johan Askling
- Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
| | - Lars Klareskog
- Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
| | - Ole Birger Pedersen
- Department of Clinical Medicine, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Immunology, Zealand University Hospital, Koge, Denmark
| | | | - Alexandra Havdahl
- Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway
- Nic Waals Institute, Lovisenberg Diaconal Hospital, Oslo, Norway
- PROMENTA Research Center, Department of Psychology, University of Oslo, Oslo, Norway
| | - Bjorn Nilsson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund, Sweden
| | - Ole A Andreassen
- NORMENT Centre, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental disorders, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Mark Daly
- Institute for Molecular Medicine, Finland, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sisse Rye Ostrowski
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Deptartment of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ingileif Jonsdottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Hilma Holm
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
| | - Agnar Helgason
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Kari Stefansson
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland.
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.
| | - Daniel F Gudbjartsson
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- School of Science and Engineering, Reykjavik University, Reykjavik, Iceland
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Mo D, Liu C, Chen Y, Cheng X, Shen J, Zhao L, Zhang J. The mitochondrial ribosomal protein mRpL4 regulates Notch signaling. EMBO Rep 2023; 24:e55764. [PMID: 37009823 PMCID: PMC10240210 DOI: 10.15252/embr.202255764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 03/07/2023] [Accepted: 03/18/2023] [Indexed: 04/04/2023] Open
Abstract
Mitochondrial ribosomal proteins (MRPs) assemble as specialized ribosome to synthesize mtDNA-encoded proteins, which are essential for mitochondrial bioenergetic and metabolic processes. MRPs are required for fundamental cellular activities during animal development, but their roles beyond mitochondrial protein translation are poorly understood. Here, we report a conserved role of the mitochondrial ribosomal protein L4 (mRpL4) in Notch signaling. Genetic analyses demonstrate that mRpL4 is required in the Notch signal-receiving cells to permit target gene transcription during Drosophila wing development. We find that mRpL4 physically and genetically interacts with the WD40 repeat protein wap and activates the transcription of Notch signaling targets. We show that human mRpL4 is capable of replacing fly mRpL4 during wing development. Furthermore, knockout of mRpL4 in zebrafish leads to downregulated expression of Notch signaling components. Thus, we have discovered a previously unknown function of mRpL4 during animal development.
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Affiliation(s)
- Dongqing Mo
- Department of Plant Biosecurity and MOA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Chenglin Liu
- Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
- College of FisheriesOcean University of ChinaQingdaoChina
- Key Laboratory of Mariculture (OUC)Ministry of EducationQingdaoChina
| | - Yao Chen
- Department of Plant Biosecurity and MOA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Xinkai Cheng
- Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
- College of FisheriesOcean University of ChinaQingdaoChina
- Key Laboratory of Mariculture (OUC)Ministry of EducationQingdaoChina
| | - Jie Shen
- Department of Plant Biosecurity and MOA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Long Zhao
- Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
- College of FisheriesOcean University of ChinaQingdaoChina
- Key Laboratory of Mariculture (OUC)Ministry of EducationQingdaoChina
| | - Junzheng Zhang
- Department of Plant Biosecurity and MOA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant ProtectionChina Agricultural UniversityBeijingChina
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6
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Kalotay E, Klugmann M, Housley GD, Fröhlich D. Recessive aminoacyl-tRNA synthetase disorders: lessons learned from in vivo disease models. Front Neurosci 2023; 17:1182874. [PMID: 37274208 PMCID: PMC10234152 DOI: 10.3389/fnins.2023.1182874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/17/2023] [Indexed: 06/06/2023] Open
Abstract
Protein synthesis is a fundamental process that underpins almost every aspect of cellular functioning. Intriguingly, despite their common function, recessive mutations in aminoacyl-tRNA synthetases (ARSs), the family of enzymes that pair tRNA molecules with amino acids prior to translation on the ribosome, cause a diverse range of multi-system disorders that affect specific groups of tissues. Neurological development is impaired in most ARS-associated disorders. In addition to central nervous system defects, diseases caused by recessive mutations in cytosolic ARSs commonly affect the liver and lungs. Patients with biallelic mutations in mitochondrial ARSs often present with encephalopathies, with variable involvement of peripheral systems. Many of these disorders cause severe disability, and as understanding of their pathogenesis is currently limited, there are no effective treatments available. To address this, accurate in vivo models for most of the recessive ARS diseases are urgently needed. Here, we discuss approaches that have been taken to model recessive ARS diseases in vivo, highlighting some of the challenges that have arisen in this process, as well as key results obtained from these models. Further development and refinement of animal models is essential to facilitate a better understanding of the pathophysiology underlying recessive ARS diseases, and ultimately to enable development and testing of effective therapies.
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Affiliation(s)
- Elizabeth Kalotay
- Translational Neuroscience Facility and Department of Physiology, School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Matthias Klugmann
- Translational Neuroscience Facility and Department of Physiology, School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
- Research Beyond Borders, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Gary D. Housley
- Translational Neuroscience Facility and Department of Physiology, School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Dominik Fröhlich
- Translational Neuroscience Facility and Department of Physiology, School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
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7
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Wang S, Kang Y, Wang R, Deng J, Yu Y, Yu J, Wang J. Emerging Roles of NDUFS8 Located in Mitochondrial Complex I in Different Diseases. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248754. [PMID: 36557887 PMCID: PMC9783039 DOI: 10.3390/molecules27248754] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/05/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022]
Abstract
NADH:ubiquinone oxidoreductase core subunit S8 (NDUFS8) is an essential core subunit and component of the iron-sulfur (FeS) fragment of mitochondrial complex I directly involved in the electron transfer process and energy metabolism. Pathogenic variants of the NDUFS8 are relevant to infantile-onset and severe diseases, including Leigh syndrome, cancer, and diabetes mellitus. With over 1000 nuclear genes potentially causing a mitochondrial disorder, the current diagnostic approach requires targeted molecular analysis, guided by a combination of clinical and biochemical features. Currently, there are only several studies on pathogenic variants of the NDUFS8 in Leigh syndrome, and a lack of literature on its precise mechanism in cancer and diabetes mellitus exists. Therefore, NDUFS8-related diseases should be extensively explored and precisely diagnosed at the molecular level with the application of next-generation sequencing technologies. A more distinct comprehension will be needed to shed light on NDUFS8 and its related diseases for further research. In this review, a comprehensive summary of the current knowledge about NDUFS8 structural function, its pathogenic mutations in Leigh syndrome, as well as its underlying roles in cancer and diabetes mellitus is provided, offering potential pathogenesis, progress, and therapeutic target of different diseases. We also put forward some problems and solutions for the following investigations.
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Affiliation(s)
- Sifan Wang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, China; (S.W.); (Y.K.); (R.W.); (J.D.); (Y.Y.)
- Department of Pathology, School of Basic Medicine, Central South University, Changsha 410008, China
- Xiangya School of Medicine, Central South University, Changsha 410013, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Yuanbo Kang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, China; (S.W.); (Y.K.); (R.W.); (J.D.); (Y.Y.)
- Department of Pathology, School of Basic Medicine, Central South University, Changsha 410008, China
- Xiangya School of Medicine, Central South University, Changsha 410013, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Ruifeng Wang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, China; (S.W.); (Y.K.); (R.W.); (J.D.); (Y.Y.)
- Department of Pathology, School of Basic Medicine, Central South University, Changsha 410008, China
| | - Junqi Deng
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, China; (S.W.); (Y.K.); (R.W.); (J.D.); (Y.Y.)
- Department of Pathology, School of Basic Medicine, Central South University, Changsha 410008, China
| | - Yupei Yu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, China; (S.W.); (Y.K.); (R.W.); (J.D.); (Y.Y.)
- Department of Pathology, School of Basic Medicine, Central South University, Changsha 410008, China
| | - Jun Yu
- Department of Neurology, Third Xiangya Hospital, Central South University, Changsha 410008, China
- Correspondence: (J.Y.); (J.W.); Tel./Fax: +86-731-84805411 (J.W.)
| | - Junpu Wang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, China; (S.W.); (Y.K.); (R.W.); (J.D.); (Y.Y.)
- Department of Pathology, School of Basic Medicine, Central South University, Changsha 410008, China
- Xiangya School of Medicine, Central South University, Changsha 410013, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Correspondence: (J.Y.); (J.W.); Tel./Fax: +86-731-84805411 (J.W.)
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8
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Cacheiro P, Westerberg CH, Mager J, Dickinson ME, Nutter LMJ, Muñoz-Fuentes V, Hsu CW, Van den Veyver IB, Flenniken AM, McKerlie C, Murray SA, Teboul L, Heaney JD, Lloyd KCK, Lanoue L, Braun RE, White JK, Creighton AK, Laurin V, Guo R, Qu D, Wells S, Cleak J, Bunton-Stasyshyn R, Stewart M, Harrisson J, Mason J, Haseli Mashhadi H, Parkinson H, Mallon AM, Smedley D. Mendelian gene identification through mouse embryo viability screening. Genome Med 2022; 14:119. [PMID: 36229886 PMCID: PMC9563108 DOI: 10.1186/s13073-022-01118-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 09/26/2022] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND The diagnostic rate of Mendelian disorders in sequencing studies continues to increase, along with the pace of novel disease gene discovery. However, variant interpretation in novel genes not currently associated with disease is particularly challenging and strategies combining gene functional evidence with approaches that evaluate the phenotypic similarities between patients and model organisms have proven successful. A full spectrum of intolerance to loss-of-function variation has been previously described, providing evidence that gene essentiality should not be considered as a simple and fixed binary property. METHODS Here we further dissected this spectrum by assessing the embryonic stage at which homozygous loss-of-function results in lethality in mice from the International Mouse Phenotyping Consortium, classifying the set of lethal genes into one of three windows of lethality: early, mid, or late gestation lethal. We studied the correlation between these windows of lethality and various gene features including expression across development, paralogy and constraint metrics together with human disease phenotypes. We explored a gene similarity approach for novel gene discovery and investigated unsolved cases from the 100,000 Genomes Project. RESULTS We found that genes in the early gestation lethal category have distinct characteristics and are enriched for genes linked with recessive forms of inherited metabolic disease. We identified several genes sharing multiple features with known biallelic forms of inborn errors of the metabolism and found signs of enrichment of biallelic predicted pathogenic variants among early gestation lethal genes in patients recruited under this disease category. We highlight two novel gene candidates with phenotypic overlap between the patients and the mouse knockouts. CONCLUSIONS Information on the developmental period at which embryonic lethality occurs in the knockout mouse may be used for novel disease gene discovery that helps to prioritise variants in unsolved rare disease cases.
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Affiliation(s)
- Pilar Cacheiro
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | | | - Jesse Mager
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Mary E Dickinson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Lauryl M J Nutter
- The Hospital for Sick Children, The Centre for Phenogenomics, Toronto, Canada
| | - Violeta Muñoz-Fuentes
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Chih-Wei Hsu
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA.,Department of Education, Innovation and Technology, Baylor College of Medicine, Houston, TX, USA
| | - Ignatia B Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA
| | - Ann M Flenniken
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, The Centre for Phenogenomics, Toronto, Canada
| | - Colin McKerlie
- The Hospital for Sick Children, The Centre for Phenogenomics, Toronto, Canada
| | | | - Lydia Teboul
- The Mary Lyon Centre, MRC Harwell Institute, Harwell, Oxfordshire, UK
| | - Jason D Heaney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - K C Kent Lloyd
- Mouse Biology Program, University of California Davis, Davis, CA, USA
| | - Louise Lanoue
- Mouse Biology Program, University of California Davis, Davis, CA, USA
| | | | | | - Amie K Creighton
- The Hospital for Sick Children, The Centre for Phenogenomics, Toronto, Canada
| | - Valerie Laurin
- The Hospital for Sick Children, The Centre for Phenogenomics, Toronto, Canada
| | - Ruolin Guo
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, The Centre for Phenogenomics, Toronto, Canada
| | - Dawei Qu
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, The Centre for Phenogenomics, Toronto, Canada
| | - Sara Wells
- The Mary Lyon Centre, MRC Harwell Institute, Harwell, Oxfordshire, UK
| | - James Cleak
- The Mary Lyon Centre, MRC Harwell Institute, Harwell, Oxfordshire, UK
| | | | - Michelle Stewart
- The Mary Lyon Centre, MRC Harwell Institute, Harwell, Oxfordshire, UK
| | - Jackie Harrisson
- The Mary Lyon Centre, MRC Harwell Institute, Harwell, Oxfordshire, UK
| | - Jeremy Mason
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Hamed Haseli Mashhadi
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | | | | | | | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London, UK.
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9
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Vafaee-Shahi M, Farhadi M, Razmara E, Morovvati S, Ghasemi S, Abedini SS, Bagher Z, Alizadeh R, Falah M. Novel phenotype and genotype spectrum of NARS2 and literature review of previous mutations. Ir J Med Sci 2022; 191:1877-1890. [PMID: 34374940 DOI: 10.1007/s11845-021-02736-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/30/2021] [Indexed: 01/19/2023]
Abstract
BACKGROUND Mutations in NARS2 (MIM: 612803) are associated with combined oxidative phosphorylation deficiency 24 (COXPD24; MIM: 616239) that is a rare mitochondrial and a multisystem autosomal recessive disorder. AIMS We aimed to detect the underlying genetic factors in two siblings with progressive ataxia, epilepsy, and severe-to-profound hearing impairment. METHODS After doing medical assessments and pertinent tests (i.e., auditory brainstem responses, pure tone otoacoustic emission test, cardiac examinations, computed tomography, and electroencephalogram), because of the clinical and probable genetic heterogeneity, whole-exome sequencing was performed, and co-segregation analysis was confirmed by Sanger sequencing. Biological impacts of the novel variant were evaluated using sequence-to-function bioinformatics tools. RESULTS A novel homozygous missense variant, NM_024678.6:c.545 T > A; p.(Ile182Lys), in exon 5 of NARS2 was identified in both patients and verified by Sanger sequencing. In silico analyses introduced this variant as pathogenic. Mitral valve prolapses with mild regurgitation, brachymetatarsia, severe hallux valgus, and clubbed fingers were reported as novel manifestations in association with NARS2 gene. By doing a literature review, we also underscored the high heterogeneity of disease phenotype. CONCLUSIONS Herein, we report some novel phenotype and genotype features of two female patients in an Iranian consanguineous family with COXPD24, caused by a variant in NARS2-NM_024678.6: c.545 T > A; p.(Ile182Lys). Moreover, our data expanded the phenotype and genotype spectrum of NARS2-related disorder and confirmed an unpredictable nature of genotype-phenotype correlation in COXPD24.
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Affiliation(s)
- Mohammad Vafaee-Shahi
- ENT and Head and Neck Research Center and Department, The Five Senses Health Institute, Hazrat Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
- Pediatric Growth and Development Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Farhadi
- ENT and Head and Neck Research Center and Department, The Five Senses Health Institute, Hazrat Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Ehsan Razmara
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Saeid Morovvati
- Department of Genetics, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Saeide Ghasemi
- Ali Asghar Children's Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Seyedeh Sedigheh Abedini
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Zohreh Bagher
- ENT and Head and Neck Research Center and Department, The Five Senses Health Institute, Hazrat Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Rafieh Alizadeh
- ENT and Head and Neck Research Center and Department, The Five Senses Health Institute, Hazrat Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Masoumeh Falah
- ENT and Head and Neck Research Center and Department, The Five Senses Health Institute, Hazrat Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran.
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10
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Analysis on the desert adaptability of indigenous sheep in the southern edge of Taklimakan Desert. Sci Rep 2022; 12:12264. [PMID: 35851076 PMCID: PMC9293982 DOI: 10.1038/s41598-022-15986-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 07/04/2022] [Indexed: 11/25/2022] Open
Abstract
The southern margin of the Taklimakan Desert is characterized by low rainfall, heavy sandstorms, sparse vegetation and harsh ecological environment. The indigenous sheep in this area are rich in resources, with the advantages of perennial estrus and good resistance to stress in most sheep. Exploring the molecular markers of livestock adaptability in this environment will provide the molecular basis for breeding research to cope with extreme future changes in the desert environment. In this study, we analyzed the population genetic structure and linkage imbalance of five sheep breeds with three different agricultural geographic characteristics using four complementary genomic selection signals: fixation index (FST), cross-population extended haplotype homozygosity (xp-EHH), Rsb (extended haplotype homozygosity between-populations) and iHS (integrated haplotype homozygosity score). We used Illumina Ovine SNP 50K Genotyping BeadChip Array, and gene annotation and enrichment analysis were performed on selected regions of the obtained genome. The ovary of Qira Black sheep (Follicular phase, Luteal phase, 30th day of pregnancy, 45th day of pregnancy) was collected, and the differentially expressed genes were screened by transcriptomic sequencing. Genome-wide selective sweep results and transcriptome data were combined for association analysis to obtain candidate genes associated with perennial estrus and stable reproduction. In order to verify the significance of the results, 15 resulting genes were randomly selected for fluorescence quantitative analysis. The results showed that Dolang sheep and Qira Black sheep evolved from Kazak sheep. Linkage disequilibrium analysis showed that the decay rate of sheep breeds in the Taklimakan Desert was higher than that in Yili grassland. The signals of FST, xp-EHH, Rsb and iHS detected 526, 332, 308 and 408 genes, respectively, under the threshold of 1% and 17 overlapping genes under the threshold of 5%. A total of 29 genes were detected in association analysis of whole-genome and transcriptome data. This study reveals the genetic mechanism of perennial estrus and environmental adaptability of indigenous sheep breeds in the Taklimakan Desert. It provides a theoretical basis for the conservation and exploitation of genetic resources of indigenous sheep breeds in extreme desert environment. This provides a new perspective for the quick adaptation of sheep and other mammals to extreme environments and future climate changes.
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11
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Wu B, Hao W, Cox MP. Reconstruction of gene innovation associated with major evolutionary transitions in the kingdom Fungi. BMC Biol 2022; 20:144. [PMID: 35706021 PMCID: PMC9202105 DOI: 10.1186/s12915-022-01346-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 06/07/2022] [Indexed: 11/26/2022] Open
Abstract
Background Fungi exhibit astonishing diversity with multiple major phenotypic transitions over the kingdom’s evolutionary history. As part of this process, fungi developed hyphae, adapted to land environments (terrestrialization), and innovated their sexual structures. These changes also helped fungi establish ecological relationships with other organisms (animals and plants), but the genomic basis of these changes remains largely unknown. Results By systematically analyzing 304 genomes from all major fungal groups, together with a broad range of eukaryotic outgroups, we have identified 188 novel orthogroups associated with major changes during the evolution of fungi. Functional annotations suggest that many of these orthogroups were involved in the formation of key trait innovations in extant fungi and are functionally connected. These innovations include components for cell wall formation, functioning of the spindle pole body, polarisome formation, hyphal growth, and mating group signaling. Innovation of mitochondria-localized proteins occurred widely during fungal transitions, indicating their previously unrecognized importance. We also find that prokaryote-derived horizontal gene transfer provided a small source of evolutionary novelty with such genes involved in key metabolic pathways. Conclusions The overall picture is one of a relatively small number of novel genes appearing at major evolutionary transitions in the phylogeny of fungi, with most arising de novo and horizontal gene transfer providing only a small additional source of evolutionary novelty. Our findings contribute to an increasingly detailed portrait of the gene families that define fungal phyla and underpin core features of extant fungi. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01346-8.
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Affiliation(s)
- Baojun Wu
- School of Natural Sciences, Massey University, Palmerston North, 4410, New Zealand.
| | - Weilong Hao
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Murray P Cox
- School of Natural Sciences, Massey University, Palmerston North, 4410, New Zealand.
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12
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Madan S, Uttekar B, Chowdhary S, Rikhy R. Mitochondria Lead the Way: Mitochondrial Dynamics and Function in Cellular Movements in Development and Disease. Front Cell Dev Biol 2022; 9:781933. [PMID: 35186947 PMCID: PMC8848284 DOI: 10.3389/fcell.2021.781933] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/16/2021] [Indexed: 01/09/2023] Open
Abstract
The dynamics, distribution and activity of subcellular organelles are integral to regulating cell shape changes during various physiological processes such as epithelial cell formation, cell migration and morphogenesis. Mitochondria are famously known as the powerhouse of the cell and play an important role in buffering calcium, releasing reactive oxygen species and key metabolites for various activities in a eukaryotic cell. Mitochondrial dynamics and morphology changes regulate these functions and their regulation is, in turn, crucial for various morphogenetic processes. In this review, we evaluate recent literature which highlights the role of mitochondrial morphology and activity during cell shape changes in epithelial cell formation, cell division, cell migration and tissue morphogenesis during organism development and in disease. In general, we find that mitochondrial shape is regulated for their distribution or translocation to the sites of active cell shape dynamics or morphogenesis. Often, key metabolites released locally and molecules buffered by mitochondria play crucial roles in regulating signaling pathways that motivate changes in cell shape, mitochondrial shape and mitochondrial activity. We conclude that mechanistic analysis of interactions between mitochondrial morphology, activity, signaling pathways and cell shape changes across the various cell and animal-based model systems holds the key to deciphering the common principles for this interaction.
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13
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Häfliger IM, Seefried FR, Spengeler M, Drögemüller C. Mining massive genomic data of two Swiss Braunvieh cattle populations reveals six novel candidate variants that impair reproductive success. Genet Sel Evol 2021; 53:95. [PMID: 34915862 PMCID: PMC8675516 DOI: 10.1186/s12711-021-00686-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 11/26/2021] [Indexed: 11/30/2022] Open
Abstract
Background This study was carried out on the two Braunvieh populations reared in Switzerland, the dairy Brown Swiss (BS) and the dual-purpose Original Braunvieh (OB). We performed a genome-wide analysis of array data of trios (sire, dam, and offspring) from the routine genomic selection to identify candidate regions showing missing homozygosity and phenotypic associations with five fertility, ten birth, and nine growth-related traits. In addition, genome-wide single SNP regression studies based on 114,890 single nucleotide polymorphisms (SNPs) for each of the two populations were performed. Furthermore, whole-genome sequencing data of 430 cattle including 70 putative haplotype carriers were mined to identify potential candidate variants that were validated by genotyping the current population using a custom array. Results Using a trio-based approach, we identified 38 haplotype regions for BS and five for OB that segregated at low to moderate frequencies. For the BS population, we confirmed two known haplotypes, BH1 and BH2. Twenty-four variants that potentially explained the missing homozygosity and associated traits were detected, in addition to the previously reported TUBD1:p.His210Arg variant associated with BH2. For example, for BS we identified a stop-gain variant (p.Arg57*) in the MRPL55 gene in the haplotype region on chromosome 7. This region is associated with the ‘interval between first and last insemination’ trait in our data, and the MRPL55 gene is known to be associated with early pregnancy loss in mice. In addition, we discuss candidate missense variants in the CPT1C, MARS2, and ACSL5 genes for haplotypes mapped in BS. In OB, we highlight a haplotype region on chromosome 19, which is potentially caused by a frameshift variant (p.Lys828fs) in the LIG3 gene, which is reported to be associated with early embryonic lethality in mice. Furthermore, we propose another potential causal missense variant in the TUBGCP5 gene for a haplotype mapped in OB. Conclusions We describe, for the first time, several haplotype regions that segregate at low to moderate frequencies and provide evidence of causality by trait associations in the two populations of Swiss Braunvieh. We propose a list of six protein-changing variants as potentially causing missing homozygosity. These variants need to be functionally validated and incorporated in the breeding program. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00686-3.
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Affiliation(s)
- Irene M Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland.
| | | | | | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland
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14
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Zhou W, Ouyang J, Li J, Liu F, An T, Cheng L, Kuo ZC, Zhang C, He Y. MRPS17 promotes invasion and metastasis through PI3K/AKT signal pathway and could be potential prognostic marker for gastric cancer. J Cancer 2021; 12:4849-4861. [PMID: 34234855 PMCID: PMC8247386 DOI: 10.7150/jca.55719] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 05/29/2021] [Indexed: 12/15/2022] Open
Abstract
In this study, the molecular mechanisms through which Mitochondrial Ribosomal Protein S17 (MRPS17) contributes to gastric cancer (GC) and its prognostic significance in GC have been explored. As a protein encoding gene, MRPS17 encodes a 28s proteins belonging the ribosomal protein S17P family. The specific roles and molecular mechanisms of MRPS17 in cancers remain ambiguous. It was revealed by analyzing data from TCGA and GEO that elevated expression of MRPS17 was significantly associated with invasion of GC and poor survival of GC patients. Then through univariate and multivariate Cox regression analyses it was demonstrated that MRPS17 an independent prognostic factor for GC patients (P<0.001). It was demonstrated by differentially expressed gene analysis and functional enrichment analysis that MPRS17 is related to PI3K/AKT pathway and Cell adhesion molecules (CAMs), while its function is mediated by collagen-containing extracellular matrix and receptor ligand/regulator activity. Then it was proven by in-vitro experiments that knocking down of MRPS17 gene in AGS and SGC7901 cells would significantly inhibit proliferation and invasion capability of these cells. Furthermore, it was revealed by cell immunofluorescence assay that as a ribosomalprotein, MRPS17 was mainly distributed in the cytoplasmic surface of cell membrane. Additionally, activation of PI3K/AKT pathway is responsible for malignant progression of glioma that was promoted by MRPS17. In conclusion, it was revealed in the present study that MRPS17 promoted invasion and metastasis of GC and potential molecular mechanisms through which it exerted its influences on GC were explored, suggesting its potential as a novel prognostic biomarker for GC.
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Affiliation(s)
- Wenjie Zhou
- Digestive Disease Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Zhenyuan Road 628, Guangming District, Shenzhen 518000, Guangdong, China.,Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Zhongshan 2nd Road 58, Yuexiu District, Guangzhou 510080, Guangdong, China
| | - Jun Ouyang
- Digestive Disease Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Zhenyuan Road 628, Guangming District, Shenzhen 518000, Guangdong, China.,Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Zhongshan 2nd Road 58, Yuexiu District, Guangzhou 510080, Guangdong, China
| | - Junqing Li
- Digestive Disease Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Zhenyuan Road 628, Guangming District, Shenzhen 518000, Guangdong, China.,Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Zhongshan 2nd Road 58, Yuexiu District, Guangzhou 510080, Guangdong, China
| | - Fangjie Liu
- Department of Hematology, The Seventh Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan 2nd Road 58, Yuexiu District, Guangzhou 510080, Guangdong, China
| | - Tailai An
- Digestive Disease Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Zhenyuan Road 628, Guangming District, Shenzhen 518000, Guangdong, China
| | - Lvjia Cheng
- Digestive Disease Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Zhenyuan Road 628, Guangming District, Shenzhen 518000, Guangdong, China.,Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Zhongshan 2nd Road 58, Yuexiu District, Guangzhou 510080, Guangdong, China
| | - Zi Chong Kuo
- Digestive Disease Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Zhenyuan Road 628, Guangming District, Shenzhen 518000, Guangdong, China
| | - Changhua Zhang
- Digestive Disease Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Zhenyuan Road 628, Guangming District, Shenzhen 518000, Guangdong, China
| | - Yulong He
- Digestive Disease Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Zhenyuan Road 628, Guangming District, Shenzhen 518000, Guangdong, China.,Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Zhongshan 2nd Road 58, Yuexiu District, Guangzhou 510080, Guangdong, China
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15
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Xu M, Yao J, Shi Y, Yi H, Zhao W, Lin X, Yang Z. The SRCAP chromatin remodeling complex promotes oxidative metabolism during prenatal heart development. Development 2021; 148:237772. [PMID: 33913477 DOI: 10.1242/dev.199026] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/12/2021] [Indexed: 12/28/2022]
Abstract
Mammalian heart development relies on cardiomyocyte mitochondrial maturation and metabolism. Embryonic cardiomyocytes make a metabolic shift from anaerobic glycolysis to oxidative metabolism by mid-gestation. VHL-HIF signaling favors anaerobic glycolysis but this process subsides by E14.5. Meanwhile, oxidative metabolism becomes activated but its regulation is largely elusive. Here, we first pinpointed a crucial temporal window for mitochondrial maturation and metabolic shift, and uncovered the pivotal role of the SRCAP chromatin remodeling complex in these processes in mouse. Disruption of this complex massively suppressed the transcription of key genes required for the tricarboxylic acid cycle, fatty acid β-oxidation and ubiquinone biosynthesis, and destroyed respirasome stability. Furthermore, we found that the SRCAP complex functioned through H2A.Z deposition to activate transcription of metabolic genes. These findings have unveiled the important physiological functions of the SRCAP complex in regulating mitochondrial maturation and promoting oxidative metabolism during heart development, and shed new light on the transcriptional regulation of ubiquinone biosynthesis.
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Affiliation(s)
- Mingjie Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Medical School of Nanjing University, Nanjing 210093, China
| | - Jie Yao
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Medical School of Nanjing University, Nanjing 210093, China
| | - Yingchao Shi
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Medical School of Nanjing University, Nanjing 210093, China
| | - Huijuan Yi
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Medical School of Nanjing University, Nanjing 210093, China
| | - Wukui Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Medical School of Nanjing University, Nanjing 210093, China
| | - Xinhua Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
| | - Zhongzhou Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Medical School of Nanjing University, Nanjing 210093, China.,MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Medical School of Nanjing University, Nanjing, 210093, China.,Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210093, China
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16
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Elesela S, Lukacs NW. Role of Mitochondria in Viral Infections. Life (Basel) 2021; 11:life11030232. [PMID: 33799853 PMCID: PMC7998235 DOI: 10.3390/life11030232] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 12/15/2022] Open
Abstract
Viral diseases account for an increasing proportion of deaths worldwide. Viruses maneuver host cell machinery in an attempt to subvert the intracellular environment favorable for their replication. The mitochondrial network is highly susceptible to physiological and environmental insults, including viral infections. Viruses affect mitochondrial functions and impact mitochondrial metabolism, and innate immune signaling. Resurgence of host-virus interactions in recent literature emphasizes the key role of mitochondria and host metabolism on viral life processes. Mitochondrial dysfunction leads to damage of mitochondria that generate toxic compounds, importantly mitochondrial DNA, inducing systemic toxicity, leading to damage of multiple organs in the body. Mitochondrial dynamics and mitophagy are essential for the maintenance of mitochondrial quality control and homeostasis. Therefore, metabolic antagonists may be essential to gain a better understanding of viral diseases and develop effective antiviral therapeutics. This review briefly discusses how viruses exploit mitochondrial dynamics for virus proliferation and induce associated diseases.
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Affiliation(s)
- Srikanth Elesela
- Department of Pathology, Michigan Medicine, Ann Arbor, MI 48109, USA
- Correspondence:
| | - Nicholas W. Lukacs
- Mary H. Weiser Food Allergy Center, Michigan Medicine, Ann Arbor, MI 48109, USA;
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Expression analysis of mammalian mitochondrial ribosomal protein genes. Gene Expr Patterns 2020; 38:119147. [PMID: 32987154 DOI: 10.1016/j.gep.2020.119147] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/14/2020] [Accepted: 09/20/2020] [Indexed: 02/07/2023]
Abstract
Mitochondrial ribosomal proteins (MRPs) are essential components for the structural and functional integrity of the mitoribosome complex. Throughout evolution, the mammalian mitoribosome has acquired new Mrp genes to compensate for loss of ribosomal RNA. More than 80 MRPs have been identified in mammals. Here we document expression pattern of 79 Mrp genes during mouse development and adult tissues and find that these genes are consistently expressed throughout early embryogenesis with little stage or tissue specificity. Further investigation of the amino acid sequence reveals that this group of proteins has little to no protein similarity. Recent work has shown that the majority of Mrp genes are essential resulting in early embryonic lethality, suggesting no functional redundancy among the group. Taken together, these results indicate that the Mrp genes are not a gene family descended from a single ancestral gene, and that each MRP has unique and essential role in the mitoribosome complex. The lack of functional redundancy is surprising given the importance of the mitoribosome for cellular and organismal viability. Further, these data suggest that genomic variants in Mrp genes may be causative for early pregnancy loss and should be evaluated as clinically.
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The people behind the papers - Agnes Cheong and Jesse Mager. Development 2020; 147:147/10/dev191536. [PMID: 32457129 DOI: 10.1242/dev.191536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Nuclear-encoded mitochondrial ribosomal proteins (MRPs) are crucial for mitochondrial function and hence cellular energy production. A new paper in Development investigates the function of MRPs in early mouse development, thanks to a battery of knockout mutants. We caught up with first author (and recent graduate) Agnes Cheong and her supervisor Jesse Mager, Associate Professor at the Department of Veterinary and Animal Sciences at the University of Massachusetts, Amherst, to find out more.
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